One issue is still in play: what type of disclosure prosecutors are required to make to defendants whose cases are "derived from" evidence gathered under section 702 of the law.

Intelligence community lawyers and experts want to make a general disclosure, to put defense lawyers on notice the program may have been helpful, so they can petition a judge and challenge the evidence gathering, in the event the 702 program played a role in putting together a prosecution. But others in the Justice Department believe defendants in each case in which the secret electronic surveillance played a role should get explicit notice of that.

The controversy matters because for years now, federal courts including the U.S. Supreme Court have ruled that only people who can prove they were subjected to surveillance can challenge the constitutionality of the 2008 law in court. By giving defendants notice they were monitored under section 702, the government would remove a major hurdle for moving a test case through the courts and ultimately, all the way up to the highest court in the land.

Late Thursday, the American Civil Liberties Union sued the Justice Department under the Freedom of Information Act. The group wants to know what the current DOJ policy is for informing criminal defendants they have been subject to electronic monitoring. The ACLU lawsuit, filed in federal court in New York, asks for records on cases where the government used information obtained from secret surveillance.

"By failing to tell defendants that they had been surveilled by the NSA under the FISA Amendments Act, the government effectively shielded its warrantless wiretapping program from judicial review. We hope this reported policy reversal will change that," said Patrick Toomey, staff attorney with the ACLU National Security Project.